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Incremental Genetic K-Means Algorithm And Its Application In Gene Expression Data Analysis, Yi Lu, Shiyong Lu, Farhad Fotouhi, Youping Deng, Susan J. Brown

Faculty Publications

Background

In recent years, clustering algorithms have been effectively applied in molecular biology for gene expression data analysis. With the help of clustering algorithms such as K-means, hierarchical clustering, SOM, etc, genes are partitioned into groups based on the similarity between their expression profiles. In this way, functionally related genes are identified. As the amount of laboratory data in molecular biology grows exponentially each year due to advanced technologies such as Microarray, new efficient and effective methods for clustering must be developed to process this growing amount of biological data.

Results

In this paper, we propose a new clustering algorithm, …

Spring Phytoplankton Photosynthesis, Growth, And Primary Production And Relationships To A Recurrent Coastal Sediment Plume And River Inputs In Southeastern Lake Michigan, Steven E. Lohrenz, Gary L. Fahnenstiel, David F. Millie, Oscar M.E. Schofield, Tom Johengon

Faculty Publications

[1] A recurrent coastal sediment plume (RCP) is an episodic event in the southern basin of Lake Michigan that typically coincides with the spring diatom bloom. Strong winter storm activity during El Nino conditions in 1998 resulted in a large and intense RCP event. Consistently higher values of the light-saturated rate of photosynthesis, P-max(B), were observed in spring 1998 compared to 1999 and 2000. Higher values of P-max(B) in 1998 appeared to be related to increased availability of phosphorus, as evidenced by significant correlations of P-max(B) with soluble reactive phosphorus (SRP). Light-saturated growth rates were also significantly correlated with SRP …

On The Approximation Of The Coriolis Terms In C-Grid Models, Dmitri A. Nechaev, Max Yaremchuk

Faculty Publications

A new representation of the Coriolis terms on the Arakawa C grid is proposed. The approximation dumps the grid-scale noise that arises because of spatial averaging of the Coriolis terms when the grid spacing is larger than the deformation radius. The proposed approximation can also be applied in C-grid schemes with semi-implicit treatment of the Coriolis terms. The new scheme is analyzed in the context of the linear inertial-gravity waves and its advantageous behavior is demonstrated with respect to the conventional technique.

Rationale For A New Generation Of Indicators For Coastal Waters, Gerald Niemi, Denice Wardrop, Robert Brooks, Susan Anderson, Valerie Brady, Hans Paerl, Chet Rakocinski, Marius Brouwer, Barbara Levinson, Michael Mcdonald

Faculty Publications

More than half the world'S human population lives within 100 km of the coast, and that number is expected to increase by 25% over the next two decades. Consequently, coastal ecosystems are at serious risk. Larger coastal populations and increasing development have led to increased loading of toxic substances, nutrients and pathogens with subsequent algal blooms, hypoxia, beach closures, and damage to coastal fisheries. Recent climate change has led to the rise in sea level with loss of coastal wetlands and saltwater intrusion into coastal aquifers. Coastal resources have traditionally been monitored on a stressor-by-stressor basis such as for nutrient …

Impacts Of A Recurrent Resuspension Event And Variable Phytoplankton Community Composition On Remote Sensing Reflectance, Trisha Bergmann, Gary Fahnenstiel, Steven Lohrenz, David Millie, Oscar Schofield

Faculty Publications

In order to characterize the impact of turbidity plumes on optical and biological dynamics, a suite of environmental parameters were measured in southern Lake Michigan during the springtime recurrent sediment plume. In-water measurements of inherent optical properties (IOPs) were entered into the Hydrolight 4.2 radiative transfer model and the output was compared with measured apparent optical properties (AOPs) across a wide range of optical conditions. Hydrolight output and measured underwater light fields were then used to clarify the effects of the sediment plume on primary production, phytoplankton community composition, and nearshore remote sensing ocean color algorithms. Our results show that …

Decadal Variability Of Circulation In The Arctic Ocean Retrieved From Climatological Data By A Variational Method, Dmitri A. Nechaev, Max Yaremchuk, Motoyoshi Ikeda

Faculty Publications

[1] An inverse 3D finite-element ocean circulation model has been designed and used to study variability of the Arctic Ocean circulation in the last 4 decades. We obtained stationary model solutions with the temperature and salinity fields close to the ones given by the Environmental Working Group (EWG) [1998] atlas. Transports at the open boundaries, wind forcing and hydrographic fields are treated as unknowns, which are varied to minimize a quadratic cost function subject to model constraints. The inverse problem is solved for 10 gridded hydrographic data sets that were obtained as winter and summer averages of EWG data over …

A New Method For Estimation Of The Sensible Heat Flux Under Unstable Conditions Using Satellite Vector Winds, Jiayi Pan, Xiao-Hai Yan, Young-Heon Jo, Quanan Zheng, W. Timothy Liu

Faculty Publications

It has been difficult to estimate the sensible heat flux at the air - sea interface using satellite data because of the difficulty in remotely observing the sea level air temperature. In this study, a new method is developed for estimating the sensible heat flux using satellite observations under unstable conditions. The basic idea of the method is that the air - sea temperature difference is related to the atmospheric convergence. Employed data include the wind convergence, sea level humidity, and sea surface temperature. These parameters can be derived from the satellite wind vectors, Special Sensor Microwave Imager (SSM/I) precipitable …

Translocation As A Strategy To Rehabilitate The Queen Conch (Strombus Gigas) Population In The Florida Keys, Gabriel A. Delgado, Claudine T. Bartels, Robert A. Glazer, Nancy J. Brown-Peterson, Kevin J. Mccarthy

Faculty Publications

Queen conch (Strombus gigas) stocks in the Florida Keys once supported commercial and recreational fisheries, but overharvesting has decimated this once abundant snail. Despite a ban on harvesting this species since 1985, the local conch population has not recovered. In addition, previous work has reported that conch located in nearshore Keys waters are incapable of spawning because of poor gonadal condition, although reproduction does occur offshore. Queen conch in other areas undergo ontogenetic migrations from shallow, nearshore sites to offshore habitats, but conch in the Florida Keys are prevented from doing so by Hawk Channel. The present study was initiated …

Seasonal Use Of Bridges By Rafinesque's Big-Eared Bat, Corynorhinus Rafinesquii, In Southern Mississippi, Austin W. Trousdale, David C. Beckett

Faculty Publications

We conducted surveys of concrete bridges in southern Mississippi from 2000–2002 to determine the phenological pattern of use by Rafinesque's big-eared bat, Corynorhinus rafinesquii. The earliest dates on which we located maternity colonies were 9 March 2000, 20 April 2001, and 15 May 2002. Maternity colonies increased in size and abundance as spring progressed. Pups were born in mid- to late May (first observed 12 May 2000, 15 May 2001, 27 May 2002) and nursed through midsummer (lactating females last captured 14 July 2000, 25 July 2001, 16 July 2002). Colony size and percentage of bridges occupied by bats declined …

Hydrogen Peroxide In Deep Waters Of The North Pacific Ocean, Jinchun Yuan, Alan M. Shiller

Faculty Publications

Hydrogen peroxide is a reactive oxygen intermediate that can play a role in a variety of redox cycles. In the ocean, it is generally considered to be dominantly photo-produced with negligible concentrations in deep waters. We have utilized a highly sensitive analytical method to investigate hydrogen peroxide in deep waters of the North Pacific Ocean. We present evidence that hydrogen peroxide exists in low nanomolar concentrations in these deep waters with an apparent minimum in the depth range of the oxygen minimum. A consideration of possible mechanisms and rates suggests both a short (similar to12 day) residence time as well …

Diel Vertical Distribution Of Atlantic Croaker, Micropogonias Undulatus, Larvae In The Northcentral Gulf Of Mexico With Comparisons To Red Drum, Sciaenops Ocellatus, Bruce H. Comyns, Joanne Lyczkowski-Shultz

Faculty Publications

Atlantic croaker Micropogonias undulates (Linnaeus, 1766) larvae < 6 mm showed a distinct pattern of vertical stratification in inner-shelf waters (< 25 m depth) of the northcentral Gulf of Mexico. Discrete-depth plankton collections were taken at night, early morning after daylight, and at mid-day or early afternoon at 1, 5, and 11–16 m. No consistent pattern among cruises was evident in the vertical stratification of Atlantic croaker larvae found in mid-day and afternoon collections, but at night the highest abundances were observed at the deepest depths sampled. Atlantic croaker larvae were least abundant in surface waters (1 m) at night. Of the 66,913 Atlantic croaker larvae collected, only 346 specimens (< 1%) were found in 1 m collections at night, and 266 of these larvae were from a single collection of large specimens (mean = 6.7 mm). By morning the vertical distribution of larvae suggested that Atlantic croaker had moved up in the water column, and highest abundances were usually found at 5 m. There was no indication that patterns of larval distribution reflected hydrographic stratification within the water column, prey availability, size of larvae, or moonlight intensity.

Effects Of Salinity On Growth And Molting Of Sympatric Callinectes Spp. From Camaronera Lagoon, Veracruz, Mexico, Sergio Cházaro-Olvera, Mark S. Peterson

Faculty Publications

Megalopae of Callinectes rathbunae Contrareras, 1930 and C. sapidus Rathbun, 1896 were exposed to salinities of 5, 15, and 25 at 25.0degreesC (through crab stage 16) to determine if there were species-specific differences in survival, growth, and intermolt duration. Survival of C. rathbunae decreased significantly at higher salinities, but there was no salinity effect for C. sapidus. Callinectes rathbunae had significantly higher survival than C. sapidus in salinities of 5 and 15, but survival was not different in a salinity of 25. There was no difference in survival of C. rathbunae by gender; survival of both genders was generally lowest …

Long-Lived Worms And Aging, Yuan Luo

Faculty Publications

Several investigators have generated long-lived nematode worms (Caenorhabditis elegans) in the past decade by mutation of genes in the organism in order to study the genetics of aging and longevity. Dozens of longevity assurance genes (LAG) that dramatically increase the longevity of this organism have been identified. All long-lived mutants of C. elegans are also resistant to environmental stress, such as high temperature, reactive oxygen species (ROS), and ultraviolet irradiation. Double mutations of some LAGS further extended life span up to 400%, providing more insight into cellular mechanisms that put limits on the life span of organisms. With …

Survey Of Salamanders In Mississippi Limestone Caves, John G. Himes, David C. Beckett, Austin W. Trousdale

Faculty Publications

During 2000-2002 we surveyed for salamanders in the larger limestone caves of Mississippi, all within the Vicksburg Group rock unit. We found four species: Plethodon mississippi was the most abundant, followed by Eurycea guttolineata, Eurycea cirrigera, and Desmognathus conanti. We did not find Pseudotriton montanus in any of the caves, and question the validity of an investigator's statement made nearly 45 years ago that, "it is one of the most numerous salamanders in Mississippi. limestone caves." The salamander fauna we found is similar to that of the only other comprehensive survey of salamanders in Mississippi caves, conducted almost thirty years …